Thirty-nine groundwater samples were collected from wells near the Tavan Tolgoi and Oyu Tolgoi mines in Mongolia and at a relatively pristine site in northern Mongolia during August to September 2013, and analyzed for the concentrations of F−, NO3−, Hg, As, Al, V, Mn, Co, Ni, Cu, Zn, Se, Mo, Cd, Sb, and Pb. A probabilistic risk assessment found that >95% of the population in the areas was at risk from drinking well water. The hazard index (HI) was >1, indicating a non-carcinogenic risk to human health. At Oyu Tolgoi, the hazard quotient (HQ) of the As concentration (mean 6.63 μg/L) was >1. At the northern site, the 95th percentile HQ was <1 but the 95th percentile HI was >1. The ratios of nitrogen and oxygen stable isotopes indicated that NO3− contamination of groundwater at Oyu Tolgoi and Tavan Tolgoi was caused by livestock waste. Mercury accumulation in livestock was examined from concentrations in livestock forage and in hair and wool samples from livestock in the South Gobi region. Sheep wool had the same level of mercury as in Japan, but camel, horse, and goat hair had high levels.